MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus

ABSTRACTThe emergence of antibiotic-resistant pathogenic bacteria within the last decades is one reason for the urgent need for new antibacterial agents. A strategy to discover new anti-infective compounds is the evaluation of the genetic capacity of secondary metabolite producers and the activation of cryptic gene clusters (genome mining). One genus known for its potential to synthesize medically important products isAmycolatopsis. However,Amycolatopsis japonicumdoes not produce an antibiotic under standard laboratory conditions. In contrast to mostAmycolatopsisstrains,A. japonicumis genetically tractable with different methods. In order to activate a possible silent glycopeptide cluster, we introduced a gene encoding the transcriptional activator of balhimycin biosynthesis, thebbrgene fromAmycolatopsis balhimycina(bbrAba), intoA. japonicum. This resulted in the production of an antibiotically active compound. Following whole-genome sequencing ofA. japonicum, 29 cryptic gene clusters were identified by genome mining. One of these gene clusters is a putative glycopeptide biosynthesis gene cluster. Using bioinformatic tools, ristomycin (syn. ristocetin), a type III glycopeptide, which has antibacterial activity and which is used for the diagnosis of von Willebrand disease and Bernard-Soulier syndrome, was deduced as a possible product of the gene cluster. Chemical analyses by high-performance liquid chromatography and mass spectrometry (HPLC-MS), tandem mass spectrometry (MS/MS), and nuclear magnetic resonance (NMR) spectroscopy confirmed thein silicoprediction that the recombinantA. japonicum/pRM4-bbrAbasynthesizes ristomycin A.

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Discovery of a Potential Liver Fibrosis Inhibitor from a Mushroom Endophytic Fungus by Genome Mining of a Silent Biosynthetic Gene Cluster

Journal of Agricultural and Food Chemistry ◽

10.1021/acs.jafc.1c03639 ◽

2021 ◽

Vol 69 (38) ◽

pp. 11303-11310

Author(s):

Jin-Tao Cheng ◽

Han-Min Wang ◽

Jia-Hui Yu ◽

Chen-Fan Sun ◽

Fei Cao ◽

...

Keyword(s):

Liver Fibrosis ◽

Gene Cluster ◽

Endophytic Fungus ◽

Genome Mining ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene

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Engineering the Erythromycin-Producing Strain Saccharopolyspora erythraea HOE107 for the Heterologous Production of Polyketide Antibiotics

Frontiers in Microbiology ◽

10.3389/fmicb.2020.593217 ◽

2020 ◽

Vol 11 ◽

Author(s):

Jin Lü ◽

Qingshan Long ◽

Zhilong Zhao ◽

Lu Chen ◽

Weijun He ◽

...

Keyword(s):

Gene Cluster ◽

Polyketide Synthase ◽

Streptomyces Coelicolor ◽

Genome Mining ◽

Bac Library ◽

Gene Clusters ◽

Artificial Chromosome ◽

Saccharopolyspora Erythraea ◽

Heterologous Production ◽

Integration Sites

Bacteria of the genus Saccharopolyspora produce important polyketide antibiotics, including erythromycin A (Sac. erythraea) and spinosad (Sac. spinosa). We herein report the development of an industrial erythromycin-producing strain, Sac. erythraea HOE107, into a host for the heterologous expression of polyketide biosynthetic gene clusters (BGCs) from other Saccharopolyspora species and related actinomycetes. To facilitate the integration of natural product BGCs and auxiliary genes beneficial for the production of natural products, the erythromycin polyketide synthase (ery) genes were replaced with two bacterial attB genomic integration sites associated with bacteriophages ϕC31 and ϕBT1. We also established a highly efficient conjugation protocol for the introduction of large bacterial artificial chromosome (BAC) clones into Sac. erythraea strains. Based on this optimized protocol, an arrayed BAC library was effectively transferred into Sac. erythraea. The large spinosad gene cluster from Sac. spinosa and the actinorhodin gene cluster from Streptomyces coelicolor were successfully expressed in the ery deletion mutant. Deletion of the endogenous giant polyketide synthase genes pkeA1-pkeA4, the product of which is not known, and the flaviolin gene cluster (rpp) from the bacterium increased the heterologous production of spinosad and actinorhodin. Furthermore, integration of pJTU6728 carrying additional beneficial genes dramatically improved the yield of actinorhodin in the engineered Sac. erythraea strains. Our study demonstrated that the engineered Sac. erythraea strains SLQ185, LJ161, and LJ162 are good hosts for the expression of heterologous antibiotics and should aid in expression-based genome-mining approaches for the discovery of new and cryptic antibiotics from Streptomyces and rare actinomycetes.

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Bioactivity-Guided Genome Mining Reveals the Lomaiviticin Biosynthetic Gene Cluster inSalinispora tropica

ChemBioChem ◽

10.1002/cbic.201300147 ◽

2013 ◽

Vol 14 (8) ◽

pp. 955-962 ◽

Cited By ~ 63

Author(s):

Roland D. Kersten ◽

Amy L. Lane ◽

Markus Nett ◽

Taylor K. S. Richter ◽

Brendan M. Duggan ◽

...

Keyword(s):

Gene Cluster ◽

Genome Mining ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene

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Identification of novel mureidomycin analogues via rational activation of a cryptic gene cluster in Streptomyces roseosporus NRRL 15998

Scientific Reports ◽

10.1038/srep14111 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 15

Author(s):

Lingjuan Jiang ◽

Lu Wang ◽

Jihui Zhang ◽

Hao Liu ◽

Bin Hong ◽

...

Keyword(s):

Gene Cluster ◽

Streptomyces Roseosporus

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Correction: Genome mining and molecular characterization of the biosynthetic gene cluster of a diterpenic meroterpenoid, 15-deoxyoxalicine B, in Penicillium canescens

Chemical Science ◽

10.1039/c6sc90012g ◽

2016 ◽

Vol 7 (3) ◽

pp. 2440-2440 ◽

Cited By ~ 1

Author(s):

Junko Yaegashi ◽

Jillian Romsdahl ◽

Yi-Ming Chiang ◽

Clay C. C. Wang

Keyword(s):

Gene Cluster ◽

Molecular Characterization ◽

Genome Mining ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

Penicillium Canescens

Correction for ‘Genome mining and molecular characterization of the biosynthetic gene cluster of a diterpenic meroterpenoid, 15-deoxyoxalicine B, in Penicillium canescens’ by Junko Yaegashi et al., Chem. Sci., 2015, 6, 6537–6544.

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Genome mining approach for harnessing the cryptic gene cluster in Alternaria solani: production of PKS–NRPS hybrid metabolite, didymellamide B

Tetrahedron Letters ◽

10.1016/j.tetlet.2016.05.043 ◽

2016 ◽

Vol 57 (25) ◽

pp. 2793-2796 ◽

Cited By ~ 8

Author(s):

Takahiro Ugai ◽

Atsushi Minami ◽

Katsuya Gomi ◽

Hideaki Oikawa

Keyword(s):

Gene Cluster ◽

Genome Mining ◽

Alternaria Solani

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Biosynthesis of a Complex Yersiniabactin-Like Natural Product via themicLocus in Phytopathogen Ralstonia solanacearum

Applied and Environmental Microbiology ◽

10.1128/aem.05198-11 ◽

2011 ◽

Vol 77 (17) ◽

pp. 6117-6124 ◽

Cited By ~ 36

Author(s):

Martin F. Kreutzer ◽

Hirokazu Kage ◽

Peter Gebhardt ◽

Barbara Wackler ◽

Hans P. Saluz ◽

...

Keyword(s):

Natural Product ◽

Gene Cluster ◽

Ralstonia Solanacearum ◽

Insertional Mutagenesis ◽

Polyketide Synthase ◽

Genome Mining ◽

Content Type ◽

A Genome ◽

Iron Deficient ◽

Peptide Synthetase

ABSTRACTA genome mining study in the plant pathogenic bacteriumRalstonia solanacearumGMI1000 unveiled a polyketide synthase/nonribosomal peptide synthetase gene cluster putatively involved in siderophore biosynthesis. Insertional mutagenesis confirmed the respective locus to be operational under iron-deficient conditions and spurred the isolation of the associated natural product. Bioinformatic analyses of the gene cluster facilitated the structural characterization of this compound, which was subsequently identified as the antimycoplasma agent micacocidin. The metal-chelating properties of micacocidin were evaluated in competition experiments, and the cellular uptake of gallium-micacocidin complexes was demonstrated inR. solanacearumGMI1000, indicating a possible siderophore role. Comparative genomics revealed a conservation of the micacocidin gene cluster in defined, but globally dispersed phylotypes ofR. solanacearum.

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